Hey, I am new to this forum and could really use some help. Back near the end of summer we were riding on our jet ski which was working fine at the time. My mother put the seat on incorrectly and I flipped it over in the middle of the lake. It got very full of water and I rode it in as quick as I could. We took the control box apart and let it dry out and everything else dried out nicely as well. Ever since that happened the jet ski is acting up. It starts up fine and runs for about 3-5 mins. Once it is warmed up and you start to ride it, it ether bogged down and stalls or bogged down right before it stalls. When you start it back up it works find again any where from 10 secs. to a mins or more. I am very confused what could be the problem. I hope its nothing major. Any help will be appreciated.

Thanks for the excellent info. The jet ski is at the lake, so as we get ready to winterize, we will check these items.
Info: We didn't get the control box completely dry because we couldn't open the spark coils. Currently the jet ski will run fine for a min., then stop running. It will start and run fine for a variable amount of time. After warmed up (> 5 min.), you may get up to 5 mins of good running then it will die. When it dies, you can hit the starter within a 1/4 sec, and the jet ski will start and run fine for another 1 to 5 mins. This condition seems to be worst if you drive the jet at near fill throttle instead of mid throttle. The water separate does not have any water in it. This seems to be a ignition problem, but I'm not certain, so looking for advice/someone's experience. For the first 5 times out after the problem started, the engine would run on 1 cylinder. Now it won't, so I haven't been able to put a ignition light on the spark plug wires to verify the problem.
Thanks!

I have a 97 waverunner and I had the same problem. Had an exhaust gasket wear out and cause water from the cooling system to leak into the engine. It was misting water into the carb, unfortunately. This caused the engine to ultimately become useless and the cylinders were thrown and began tapping the spark plugs. Needless to say I had to swap it out. So check everything you can but, from experience, I wouldn't expect too much. Granted this was a remanufactured engine that was on it when I bought it so it didn't have everything going for it (luckly I had another engine but that's another story). But all the same, it may just be done.
Good luck though!
Oh, another note, check the plugs for spark, and if the filter is clogged. Other than that, if it's gotten water in it, just run it as long and as hard as you can when it's running. But stay close to shore bc if it's like mine you may get stranded in the middle of the lake. LOL
Hope that helps and again, good luck!